tbuckley/cabot-search huggingface dataset:
METB-13. A SINGLE-CELL GENETIC IN VIVO LINEAGE-TRACING PLATFORM FOR MEDULLOBLASTOMA
Authors: Jangham Jung, Bohyeon Yu, Owen Hoare, Aaron Diaz
Journal: Neuro-Oncology (2023)

Abstract Comparative single-cell studies of group 3/4 medulloblastomas (MBs) and fetal brain have identified a common hierarchy of glutamatergic-lineage cell types and an apparent cell-of-origin in the rhombic lip. An increased understanding of the genetic regulators of stem-cell maintenance and differentiation in MB would clearly be of therapeutic benefit. There is a significant need for lineage-tracing systems to model MB malignant transformation, progression, and response to therapy. We developed in vivo and in organoid genetic lineage-tracing systems with a single-cell readout. A high-complexity lentiviral library expressing heritable polyadenylated molecular barcodes was transduced into D283 and D425 patient-derived cell lines. Barcoded cells were injected into the brains of immunocompromised mice. Both preimplantation barcoded cultures and the resulting mature tumors were profiled by single-cell RNA-sequencing (scRNA-seq). This captured both endogenous RNA and barcode transcripts. While only minimal barcode clash was detected in the preimplantation cultures, we observed a clonal expansion of barcodes in mature tumors which aligned with phylogenetics analysis of expressed mutations in endogenous RNA. Methods for assessing lineage coupling between transcriptional clusters and inferring their lineage relationship were developed. Ongoing efforts to recover barcodes from tumor sections via spatial transcriptomics will be presented. These studies fill a gap in status quo models of MB which are needed to leverage recent findings derived from single-cell analysis of human tumors.
LGG-07. TARGETED THERAPY IN PEDIATRIC LOW-GRADE GLIOMAS; REAL WORLD DATA IN THE CONTEXT OF CONVENTIONAL TREATMENT MODALITIES
Authors: David Sumerauer, Katerina Trkova, Miroslav Koblizek, Martin Kyncl, Lenka Krskova, Vladimir Benes, Michal Zapotocky
Journal: Neuro-Oncology (2023)

Abstract Progressive inoperable pediatric low-grade gliomas (pLGG) are challenging and chemotherapy provides unsatisfactory long-term disease control. Majority of pLGGs harbor oncogenic MAPK pathway alterations. BRAF and MEK inhibitors were developed and available data suggest possible benefit in pLGG patients. Therefore, we aimed to evaluate efficacy and toxicity of dabrafenib in BRAF-V600E positive pLGG and trametinib in KIAA1549::BRAF fused or NF1-associated pLGGs. Retrospective review of patients with molecularly profiled pLGGs treated with MAPK inhibitors at our institutions was performed. Response to targeted therapies was evaluated using RAPNO criteria and volumetric analysis. Twenty-six patients were eligible for this study because they had either BRAF-V600E pLGG treated with dabrafenib (n=11) or KIAA1549::BRAF fused/NF1-associated pLGG treated with trametinib (n=15) outside clinical trials. Patients received targeted therapy because of radiological progression (n=18), clinical deterioration (n=2) or as an upfront approach (n=6). Overall response rate (ORR) of the whole cohort using RAPNO criteria was 46.1% (12/26). There was a discordance observed between RAPNO bidimensional and manual volumetric analysis in 7 patients (26.9%). Progression free survival (PFS) at 2 years for the whole evaluated cohort was 78.5%(95 CI, 63.2 to 97.4%). ORR of patients with BRAF-V600E pLGG was 64% (median time to response 2.6 months). Out of fifteen patients treated with trametinib, 33% achieved partial response (median time to response 6.6 months). In total, 6 patients experienced progression on therapy. Six patients were treated with vinca alkaloids and trametinib with no additional toxicity. All 15 patients experienced trametinib-related adverse event, grade III was reported in 6 (40%) of them. Altogether 11 patients (73%) required dose reductions or treatment interruptions. MAPK inhibitors represent novel treatment modality in pLGG patients with clinical benefit in proportion of patients. Nevertheless, patients may experience progression on therapy requiring further management.
IMMU-05. TUMOR INFLAMMATION-ASSOCIATED NEUROTOXICITY (TIAN): A TOXICITY SYNDROME IN PATIENTS TREATED WITH IMMUNOTHERAPY FOR CENTRAL NERVOUS SYSTEM TUMORS
Authors: Jasia Mahdi, Jorg Dietrich, Karin Straathof, Claire Roddie, Brian Scott, Tom Belle Davidson, Laura Prolo, Tracy Batchelor, Cynthia Campen, Kara Davis, Juliane Gust, Michael Lim, Robbie Majzner, Julie Park, Sonia Partap, Sneha Ramakrishna, Rebecca Richards, Liora Schultz, Nicholas Vitanza, Leo Wang, Crystal Mackall, Michelle Monje
Journal: Neuro-Oncology (2023)

Abstract Immunotherapies have transformed the therapeutic landscape for various cancer indications; currently several preclinical and clinical studies are exploring immune-based therapies for the treatment of central nervous system (CNS) tumors. The recognition of toxicity syndromes and establishment of toxicity grading scales for cytokine release syndrome (CRS) and immune effector-cell associated neurotoxicity syndrome (ICANS) have improved the administration and management of chimeric antigen receptor (CAR)-based therapies for B cell malignancies. We have observed a localized neurotoxicity syndrome, distinct from CRS and ICANS, in patients treated with immunotherapies for CNS tumors, which we term tumor inflammation-associated neurotoxicity (TIAN). TIAN arises secondary to localized inflammation at the tumor site causing local neuronal dysfunction and/or local inflammation-induced edema leading to tissue shifts and increased intracranial pressure (ICP). Although TIAN can be associated with inflammation-induced tumoral edema and may share similarities with “pseudoprogression,” TIAN can also occur in the absence of edema due to neural-immune interactions causing primary local neural dysfunction. We distinguish two types of TIAN:1) type 1 TIAN occurs when tumor inflammation-induced edema leads to mechanical space constraints and results in increased ICP, hydrocephalus, and if unmanaged, may cause a herniation syndrome 2) type 2 TIAN reflects inflammation-induced local neural electrophysiological dysfunction resulting in transient worsening/development of new neurological symptoms. In order to facilitate the safe administration of immunotherapies for CNS tumors and standardize reporting and clinical management, we have proposed a TIAN grading scale that encompasses both types of TIAN. Even though type 1 TIAN typically consists of higher-grade toxicities than type 2 TIAN, high-grade toxicities can also be seen in type 2 TIAN when tumor inflammation affects critical cardiopulmonary functions. As the promise of immunotherapies for the treatment of CNS tumors materializes, recognizing TIAN as a distinct, local neurotoxicity syndrome will be essential for patient safety and clinical management.
MDB-21. THE OTX2-REGULATED ALTERNATIVE SPLICING LANDSCAPE CONTROLS DIFFERENTIATION AND RECONSTITUTES THE DEVELOPMENTAL ORIGINS OF GROUP 3 MEDULLOBLASTOMA
Authors: Olivier Saulnier, Jamie Zagozewski, Lisa Liang, Liam D Hendrikse, Victor Gordon, Kimberly A Aldinger, Parthiv Haldipur, Stephanie Borlase, Ludivine Coudiere-Morrison, Paul Layug, Ting Cai, Christopher J Porter, Stephane Richard, Brad W Doble, Kathleen J Millen, Michael D Taylor, Tamra E Werbowetski-Ogilvie
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor with Group 3 MB exhibiting the worst prognosis. Overexpression/amplification of OTX2 is a molecular hallmark of Group 3 MB and is primarily known to control tumor growth through regulation of cell cycle. Here, we utilized mass spectrometry and RNA-sequencing to report a non-canonical role for OTX2 in regulating alternative splicing. RNA-sequencing conducted on two OTX2-silenced Group 3 MB tumorsphere models identified 48 differentially spliced genes (DSG) associated with RNA processing, splicing and neurodevelopment that were common between both cell lines. Further interrogation of the OTX2-regulated DSGs revealed that 15 are also significantly correlated with OTX2 expression in a set of Group 3/Group 4 MB patient samples. Pseudotime mapping of the developmental trajectories of the DSGs onto the developing rhombic lip (RL) revealed significant overlap with RL lineages, including the majority of the 15 shared OTX2-regulated DSGs. We then functionally validated specific alternatively spliced exons of two DSGs, PPHLN1 and MADD which represent “early” and “late” RL developmental stages, respectively. PPHLN1 and MADD splice-blocking morpholinos were utilized to drive exon skipping and recapitulate splicing events identified in OTX2-silenced or OTX2-wildtype tumorspheres. Exon skipping altered tumorigenic properties of Group 3 MB cells in vitro, including tumorsphere size and number. Additionally, intracerebellar injections of Group 3 MB cells treated with PPHLN1 morpholino impaired tumor initiation and growth in vivo. Further breakdown of Group 3/Group 4 MBs by PPHLN1 and MADD percent spliced in (PSI) revealed that the PPHLN1 high/MADD low PSI signature observed in our OTX2 wildtype tumorspheres is associated with the most aggressive and primitive Group 3g subtype. Together, our findings reveal a previously unrecognized regulatory role for OTX2 in controlling Group 3 MB AS and offer fresh opportunities to exploit MB-specific AS events therapeutically to abrogate tumor progression.
MDB-25. LARGE CELL/ANAPLASTIC MEDULLOBLASTOMA REPRESENTS MORE THAN ONE DISEASE ENTITY
Authors: Katharina Krause, Tobias Goschzik, Evelyn Doerner, Torsten Pietsch
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma (MB) with predominant large cell or anaplastic cytological features have been identified to be associated to an aggressive clinical course and poor survival. Because cases can show mixed cytologies, these histologically defined MB types were merged in the recent WHO classification of tumors of the CNS to large cell/anaplastic (LC/A) MB. In this study, we collected FFPE samples of 137 LC/A MB of all age groups (0-39 years) diagnosed at the DGNN Brain Tumor Reference Center in Bonn, Germany, and performed a comprehensive histological, immunophenotypical, genetic and epigenetic analysis by next-generation panel sequencing (NGS), 450k/850k methylation bead-array hybridization and molecular inversion probe (MIP) technology. 73% of cases showed predominant anaplastic histology, 27% predominant large cell histology. Methylation-based subtyping and sequencing showed that the cohort of LC/A MB represented different biological entities: 6% WNT-MB, 7% SHH-MB-TP53-wildtype, 10% SHH-MB-TP53-mutant, and 77% non-WNT/non-SHH MB (with predominant epigenetic subtype II). High-resolution copy number profiling by MIP demonstrated MYC amplification in 40% of non-WNT/non-SHH MB. MYC amplification was highly associated to infant disease and predominant large cell histology. On the contrary, predominant anaplastic histology was highly associated to non-infant disease, MYCN amplification and SHH activation. By NGS we detected recurrent mutations in 37 MB-related genes; the frequency of mutations of individual MB-related genes differed significantly between the histologically and genetically defined MB types. Our data clearly demonstrate that large cell MB and anaplastic MB represent different biological entities. Therefore, and also in respect to the future development of targeted treatment approaches to these highly malignant MB types, they should be precisely diagnosed as separate MB entities.
IMMU-15. PHASE I TRIAL OF GD2.CART-CELLS AUGMENTED WITH A CONSTITUTIVELY ACTIVE INTERLEUKIN-7 RECEPTOR (C7R) FOR TREATMENT OF HIGH-GRADE PEDIATRIC CNS TUMORS
Authors: Frank Lin, Austin Stuckert, Candise Tat, Karen Moeller, Mark White, Lucia Ruggieri, Huimin Zhang, Holly Lindsay, Patricia Baxter, Fatema Malbari, Guillermo Aldave, Murali Chintagumpala, D Williams Parsons, Malcolm Brenner, Helen Heslop, Cliona Rooney, Bilal Omer
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Treatment of pediatric CNS tumors with T-cells modified with chimeric antigen receptors (CARTs) provides an innovative approach. We employ GD2-directed CART-cells (GD2.CARTs) modified to express a constitutively active interleukin-7 receptor (C7R) to increase GD2.CART survival and function independent of external cytokines, thereby augmenting activity against GD2-expressing CNS malignancies. METHODS In a Phase I study, we investigated the safety of intravenous GD2.CART therapy for pediatric patients with H3K27-altered diffuse midline glioma (DMG) or other GD2-expressing recurrent CNS tumors. We used a 3 + 3 design in which the first treatment cohort received GD2.CARTs without C7R, while subsequent cohorts received GD2.CARTs co-transduced with C7R (C7R-GD2.CARTs) at two dose levels. As a secondary endpoint we measured disease response 6 weeks after CART infusion. RESULTS 12 patients were treated without dose limiting toxicity. The first cohort (n=3: thalamic DMG, spinal DMG, recurrent AT/RT) received GD2.CARTs without C7R at 1x107 cells/m2. No toxicity was observed and all 3 patients had clinical neurological improvement lasting approximately 4 weeks before disease progression. The next two cohorts received C7R-GD2.CARTs at 1x107 cells/m2 (n=3) and 3x107 cells/m2 (n=6). Mild tumor inflammation associated neurotoxicity was observed in 7 of 9 (78%) patients, which was controlled with anakinra without need for corticosteroids. Cytokine release syndrome (CRS) was observed in 5 of 9 (56%) cases [grade 1 (n=4), grade 3 (n=1)], resolving with tocilizumab. Eight of 9 patients receiving C7R-GD2.CARTs had clinical improvement or stability for more than 8 weeks (up to 10 months at last follow-up) and received repeat cell infusions at 6 week intervals (range 2-4 cycles). Partial radiologic responses were confirmed for 2 of 7 (29%) patients with DMG. CONCLUSION Intravenous treatment with C7R-modified GD2.CARTs was well tolerated in children with CNS tumors, and the duration of clinical improvement was extended by C7R co-expression.
METB-07. MINIMALLY-INVASIVE DIAGNOSIS OF DIFFUSE LEPTOMENINGEAL GLIONEURONAL TUMOR (DLGNT) USING CEREBROSPINAL FLUID CELL-FREE DNA SEQUENCING IN PEDIATRIC AND YOUNG ADULT PATIENTS
Authors: Alexandra Giantini Larsen, Katherine Hill, Richard Hickman, Tejus Bale, Bridget Holle, Ingo Mellinghoff, Ira Dunkel, Mark Souweidane, Jeffrey Greenfield, Sameer Farouk Sait, Alexandra Miller, Matthias Karajannis
Journal: Neuro-Oncology (2023)

Abstract Diffuse leptomeningeal glioneuronal tumor (DLGNT) presents with nodular leptomeningeal disease throughout the neuroaxis. Histology shows variable presence of a low density intraparenchymal lesion containing OLIG2-expressing neoplastic cells. Molecularly, DLGNT is characterized by the presence of KIAA1549::BRAF fusion and chromosome arm 1p deletion. Concomitant gain of chromosome arm 1q is associated with poor prognosis. Diagnosis by meningeal biopsy is often non-diagnostic and we hypothesized analysis of cell free DNA (cfDNA) from cerebrospinal fluid (CSF) could represent a superior diagnostic modality. We analyzed CSF samples from 7 patients, median age of 18 years, with DLGNT including matched germline DNA. MSK-IMPACT, a hybridization capture-based next-generation DNA sequencing panel, was utilized to analyze the DNA. Prior tissue biopsy was done in 5/7 patients. Of these, biopsy was non-diagnostic in 3 patients and positive for the KIAA1549:BRAF fusion in 2. Analysis of CSF cfDNA detected KIAA1549::BRAF fusion in 5/7 (71%) of patients, including all patients with prior non-diagnostic biopsy or tissue quantity insufficient for molecular testing. Analysis of CSF cfDNA copy number profiles revealed 1p-/1q+ in 6 patients and 1p- only in the remaining 1 patient, fully concordant with available prior tissue testing in all instances. In 2 patients with prior tissue-confirmed KIAA1549::BRAF fusion, the fusion was not detected in CSF cfDNA during/after treatment with a MEK inhibitor, but additional somatic alterations and DNA copy number profiles were similar to the prior biopsies. Additional somatic alterations were identified in ATRX, BCOR, RARA, STAT5A, SPOP, PPM1D, MED12, KMT2C, RECQL and SETD2, including likely oncogenic secondary driver alterations that have not been previously reported in DLGNT. Given the high molecular diagnostic yield and concordance with open biopsy, cfDNA CSF sequencing should be considered as a first line diagnostic maneuver for patients with MRI findings suspicious for DLGNT, followed by open biopsy only if CSF is non-diagnostic.
METB-06. HIGH FREQUENCY OF CLINICALLY RELEVANT ALTERATIONS DETECTED BY INTEGRATED TUMOR AND GERMLINE GENE PANEL TESTING IN CHILDREN WITH CNS TUMORS – RESULTS FROM THE TEXAS KIDSCANSEQ STUDY
Authors: Frank Y Lin, Lauren Desrosiers, Ross Mangum, Jacquelyn Reuther, Carrie Mohila, Melissa M Blessing, Guillermo Aldave, Donna M Muzny, Juan Carlos Bernini, Jonathan Gill, Timothy Griffin, Gail Tomlinson, Kelly Vallance, Murali M Chintagumpala, Sarah Scollon, Dolores H López-Terrada, Kevin E Fisher, Angshumoy Roy, Sharon E Plon, D Williams Parsons
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Tumor and germline alterations detected by sequencing have the potential to inform management of children with CNS tumors. Comparative clinical utility data for available molecular sequencing modalities are needed to optimize testing strategies. METHODS Cancer patients less than 18 years of age were eligible to enroll in the Texas KidsCanSeq (KCS) clinical genomics study at six Texas institutions. Blood testing was performed on all patients using a pediatric solid tumor targeted DNA panel (124 genes), which included 35 genes associated with known cancer predisposition syndromes. Tumor testing was conducted on high-risk or recurrent tumors using the same DNA panel as well as an 81-gene RNA fusion panel. Tumor variants were classified as being of strong (Tier 1) or potential (Tier 2) clinical significance following AMP/ASCO/CAP guidelines. Germline pathogenic (P) or likely pathogenic (LP) variants per ACMG/AMP guidelines were considered clinically relevant. RESULTS A total of 224 children with CNS tumors were enrolled, including 146 patients with high-risk or recurrent tumors. Tissues were sufficient for analysis from 132 tumors and 211 germline samples. Clinically relevant alterations were identified in 90 of 132 (68%) tumors tested. Of 50 with therapeutic implications, 21 (42%) were not known from prior clinical testing. Therapeutically relevant tumor variants most frequently involved BRAF (n=20), CDKN2A/B (n=16), SMARCB1 (n=9), PIK3CA (n=8), and NF1 (n=7). One high grade glioma (in a patient with Lynch syndrome) was found to be hypermutated (tumor mutation burden &amp;gt;190 mut/Mb). Germline analysis detected P/LP variants in cancer predisposition genes in 25 of 211 (12%) patients tested, including 12 of 135 (9%) with high-risk/recurrent tumors. CONCLUSION Combined tumor and germline panel testing revealed alterations of clinical relevance according to consensus guidelines in approximately 70% of children with high-risk or recurrent CNS tumors.
NCCN Guidelines® Insights: Breast Cancer, Version 4.2023
Authors: William J. Gradishar, Meena S. Moran, Jame Abraham, Vandana Abramson, Rebecca Aft, Doreen Agnese, Kimberly H. Allison, Bethany Anderson, Harold J. Burstein, Helen Chew, Chau Dang, Anthony D. Elias, Sharon H. Giordano, Matthew P. Goetz, Lori J. Goldstein, Sara A. Hurvitz, Rachel C. Jankowitz, Sara H. Javid, Jairam Krishnamurthy, A. Marilyn Leitch, Janice Lyons, Joanne Mortimer, Sameer A. Patel, Lori J. Pierce, Laura H. Rosenberger, Hope S. Rugo, Bryan Schneider, Mary Lou Smith, Hatem Soliman, Erica M. Stringer-Reasor, Melinda L. Telli, Mei Wei, Kari B. Wisinski, Jessica S. Young, Kay Yeung, Mary A. Dwyer, Rashmi Kumar
Journal: Journal of the National Comprehensive Cancer Network (2023)

The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Breast Cancer address all aspects of management for breast cancer. The treatment landscape of metastatic breast cancer is evolving constantly. The therapeutic strategy takes into consideration tumor biology, biomarkers, and other clinical factors. Due to the growing number of treatment options, if one option fails, there is usually another line of therapy available, providing meaningful improvements in survival. This NCCN Guidelines Insights report focuses on recent updates specific to systemic therapy recommendations for patients with stage IV (M1) disease.
Private Payer and Medicare Coverage Policies for Use of Circulating Tumor DNA Tests in Cancer Diagnostics and Treatment
Authors: Michael P. Douglas, Meera V. Ragavan, Cheng Chen, Anika Kumar, Stacy W. Gray, Collin M. Blakely, Kathryn A. Phillips
Journal: Journal of the National Comprehensive Cancer Network (2023)

Background: Circulating tumor DNA (ctDNA) is used to select initial targeted therapy, identify mechanisms of therapeutic resistance, and measure minimal residual disease (MRD) after treatment. Our objective was to review private and Medicare coverage policies for ctDNA testing. Methods: Policy Reporter was used to identify coverage policies (as of February 2022) from private payers and Medicare Local Coverage Determinations (LCDs) for ctDNA tests. We abstracted data regarding policy existence, ctDNA test coverage, cancer types covered, and clinical indications. Descriptive analyses were performed by payer, clinical indication, and cancer type. Results: A total of 71 of 1,066 total policies met study inclusion criteria, of which 57 were private policies and 14 were Medicare LCDs; 70% of private policies and 100% of Medicare LCDs covered at least one indication. Among 57 private policies, 89% specified a policy for at least 1 clinical indication, with coverage for ctDNA for initial treatment selection most common (69%). Of 40 policies addressing progression, coverage was provided 28% of the time, and of 20 policies addressing MRD, coverage was provided 65% of the time. Non–small cell lung cancer (NSCLC) was the cancer type most frequently covered for initial treatment (47%) and progression (60%). Among policies with ctDNA coverage, coverage was restricted to patients without available tissue or in whom biopsy was contraindicated in 91% of policies. MRD was commonly covered for hematologic malignancies (30%) and NSCLC (25%). Of the 14 Medicare LCD policies, 64% provided coverage for initial treatment selection and progression, and 36% for MRD. Conclusions: Some private payers and Medicare LCDs provide coverage for ctDNA testing. Private payers frequently cover testing for initial treatment, especially for NSCLC, when tissue is insufficient or biopsy is contraindicated. Coverage remains variable across payers, clinical indications, and cancer types despite inclusion in clinical guidelines, which could impact delivery of effective cancer care.